VILL

villin like, the group of Gelsolin/villins

Basic information

Region (hg38): 3:37988059-38007188

Links

ENSG00000136059 ∙ NCBI:50853 ∙ OMIM:619666 ∙ HGNC:30906 ∙ Uniprot:O15195 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VILL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VILL gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			57	4	1	62
nonsense						0
start loss						0
frameshift				2		2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	57	7	1

Variants in VILL

This is a list of pathogenic ClinVar variants found in the VILL region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-37993949-G-A		not specified	Uncertain significance (Aug 12, 2021)
3-37993959-A-G		not specified	Uncertain significance (Dec 06, 2022)
3-37994295-C-T		not specified	Uncertain significance (Nov 15, 2021)
3-37994346-G-A		not specified	Uncertain significance (Nov 16, 2022)
3-37994369-C-T		not specified	Uncertain significance (Oct 02, 2023)
3-37994376-A-C		not specified	Uncertain significance (Sep 27, 2021)
3-37994390-G-C		not specified	Uncertain significance (Jun 01, 2023)
3-37994426-G-A		not specified	Uncertain significance (Jul 30, 2023)
3-37994430-C-A		not specified	Uncertain significance (Aug 02, 2022)
3-37994459-G-A		not specified	Uncertain significance (Jul 13, 2022)
3-37995751-A-T			Likely benign (Feb 01, 2024)
3-37995764-G-A		not specified	Uncertain significance (Nov 23, 2021)
3-37995774-A-T		not specified	Uncertain significance (Feb 15, 2023)
3-37995812-C-T		not specified	Uncertain significance (Jan 18, 2022)
3-37997077-G-A		not specified	Uncertain significance (Jun 09, 2022)
3-37997158-C-A		not specified	Uncertain significance (May 26, 2023)
3-37997508-G-A		not specified	Likely benign (May 31, 2023)
3-37997516-G-A		not specified	Uncertain significance (Oct 25, 2023)
3-37997519-C-T		not specified	Uncertain significance (Dec 13, 2023)
3-37997520-G-A		not specified	Uncertain significance (Dec 26, 2023)
3-37997532-G-A		not specified	Uncertain significance (Mar 25, 2024)
3-37997568-C-T		not specified	Uncertain significance (Sep 06, 2022)
3-37997575-C-A		not specified	Uncertain significance (Mar 24, 2023)
3-37997607-G-A		not specified	Uncertain significance (Sep 26, 2023)
3-37997612-G-T		not specified	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VILL	protein_coding	protein_coding	ENST00000283713	19	19130

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.91e-23	0.0156	125170	4	574	125748	0.00230

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.345	485	507	0.957	0.0000285	5610
Missense in Polyphen		143	153.78	0.92991		1838
Synonymous	0.666	192	204	0.941	0.0000117	1658
Loss of Function	1.04	39	46.7	0.836	0.00000234	496

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0104	0.0103
Ashkenazi Jewish	0.000497	0.000496
East Asian	0.00417	0.00409
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.00113	0.00112
Middle Eastern	0.00417	0.00409
South Asian	0.00510	0.00504
Other	0.00262	0.00261

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible tumor suppressor.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.958
• rvis_EVS: -1.5
• rvis_percentile_EVS: 3.57

Haploinsufficiency Scores

• pHI: 0.370
• hipred: N
• hipred_score: 0.172
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.359

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Vill

Gene ontology

• Biological process: cytoskeleton organization;actin filament capping
• Cellular component: actin cytoskeleton
• Molecular function: structural constituent of cytoskeleton;actin filament binding